Reader for SAM alignment files. More...

Inheritance diagram for shore::sam_reader:

Public Member Functions
	sam_reader (const std::string &fn, const config &c, shore::alignment::cmp_type cmp=shore::alignment::cmp_null)

bool	has_data ()

const shore::alignment &	current () const

void	next ()

const std::string &	current_line () const

void	set_range (const shore::refseq_coor &s, const shore::refseq_coor &e, const long maxrl=0l)

Public Member Functions inherited from shore::sam_base
	sam_base (const config &c)

leftover_pipe &	leftovers ()

void	set_max_ed (const int ed)

void	set_max_gaps (const int g)

void	set_max_gapsize (const int g)

void	set_max_hits (const int h)

void	discard_softclipped (const bool d)

Additional Inherited Members
Static Public Member Functions inherited from shore::sam_base
static void	cigar2aln (std::string &aln, cigarstats &cs, const std::string &read, const std::string &cigar, const shore::sequence_record &chr, const size_t start, const int max_gapsize=1)
	Convert cigar string to shore alignment string. More...

Protected Types inherited from shore::sam_base
typedef std::map< std::string, size_t >::const_iterator	ichr_t

Protected Member Functions inherited from shore::sam_base
void	load_reference ()
	Load the reference sequence.

void	xa_parse (shore::alignment &f, std::string &seq, std::string &cigar, bool &isrev, cigarstats &cigsta, size_t &xaofs, const std::string &xa)
	Parse BWA style XA tags.

Protected Attributes inherited from shore::sam_base
config	m_conf

std::pair< int, shore::alignment::InsertState >	m_peconv [0x801]
	SAM flag to SHORE PE flag conversion table.

std::pair< int, shore::read::InsertState >	m_peconv_left [0x801]
	SAM flag leftover SHORE PE flag conversion table.

int	m_tid [256][256]
	Lookup table for tag enumeration.

shore::sink< samheader, std::string >	m_header

std::map< std::string, size_t >	m_refmap
	Maps string refseq IDs to fasta enumerated IDs.

std::vector < shore::sequence_record >	m_refseq
	Reference sequences.

std::vector< int >	m_bamid2seqid
	Converts bam file sequence IDs to fasta enumerated IDs.

Static Protected Attributes inherited from shore::sam_base
static const int	MAXTAGS =3224
	Maximum number of tags ([A-Za-z][A-Za-z0-9]) = 3224.

Detailed Description

Reader for SAM alignment files.

The documentation for this class was generated from the following file:

Public Types